Synopsis:
All over seventeenth-century Europe, catastrophes are taking place. Strange natural conditions, such as blood-red skies and even earthquakes in York, are provoking panic in England, and reports show that the phenomena are happening all over the Earth. Many believe it is the beginning of the Apocalypse. Sir Stephen Strange, the court magician of Queen Elizabeth I (replacing John Dee, Elizabeth's historical court magician), senses that there are unnatural forces at work. He thinks that it is somehow linked to the "Virginia Maid", a ship that carries Virginia Dare and her hulking native American bodyguard Rojhaz (who is strangely pale-skinned and blonde-haired). Virginia is the first child born in the English colony of Roanoke. She has strange shapeshifting powers, and Strange suspects she is the cause of the disastrous weather.

At the same time, there is a race for the legendary treasure of the Knights Templar, thought to be a weapon of unlimited power. The Queen's head of intelligence, Sir Nicholas Fury, finds himself pitted against the powerful Otto von Doom, the sinister Count of Latveria.

James VI of Scotland lusts after the Queen's throne. He collaborates with Spanish High Inquisitor Enrique and Count Doom to assassinate Queen Elizabeth and blame the "witchbreed" of Carlos Javier for the crime. The murder succeeds and James of Scotland becomes King of England.

Sir Stephen then finds himself on the moon where he meets the Watcher, who tells him that the strange events are due to an anomaly he calls the Forerunner. The Forerunner is from the future and his presence in the past has disrupted reality to the point of impending multi-universal annihilation. Despite telling Sir Stephen of his own free will, the Watcher forces Stephen to enter a pact that will not allow him to repeat what he has learned for as long as he lives.

Sir Stephen, Sir Nicholas and Javier betray King James to save the universe. Fury, Javier and his "witchbreed" launch a successful attack on Count Doom's fortress, retrieve the Templars' treasure (Thor's Hammer, wielded by a pilgrim called Donal) and liberate Otto's captives, the superpowered quartet known as the Four from the Fantastick. They then flee to the New World.

Meanwhile, in Spain, Enrique the Grand Inquisitor is betrayed along with his young acolytes, Petros and Sister Wanda. All three of them are "witchbreed" themselves and have only killed those that could not pass off as human. At the moment of execution, however, they turn the tide on their enemies and escape on board a ship bound for America.

Sir Stephen Strange is executed by James, and his head put on a pike. With his magic his spirit can still communicate in a telepathic way. His wife Clea takes his head from the pike and sets off for America with Virginia and Rojhaz. Clea believes that it is not Virginia who is the Forerunner but her muscle-bound, white-skinned, blond-haired, blue-eyed "Native American" companion.

"Rojhaz" is none other than Steve Rogers, a.k.a. Captain America, who was atomized by a fascist US government in a dystopian future. His "destruction" (i.e. he disappeared from the normal timeline, but reappeared in this timeline) caused the rift that is destroying the universe. It also meant that a lot of the heroes and villains who were not due to appear for another 350 years have turned up early in order, so the Watcher believes, to counter the Forerunner's negative effects.

In order to close the rift, Rogers is sent back, along with Sir Nicholas Fury. Donal opens the rift with his lightning, and Enrique controls it with his magnetic powers, based on the theories of Sir Richard Reed. The universe restores itself, and Uatu, the Watcher, is granted a "pocket universe" in which the 1602 timeline remains intact.